Support for additional seperate ship/weapon/etc. tables. Similar to I-war 2's method. Essentially, in I-War 2 every ship/weapon/projectile/etc. has it's own .ini file packed into one large Zip file. Sim's are created from the information in their .ini file just as in Freespace.
This would completely eliminate the problem of different mods 'fighting' over the ships and weapons tables as they could create their own unique ships and only need to include those with the mod allowing them to be seamlessly integrated with the official content. Since Freespace's editor is not script-based (In I-War the resource file for new sims is directly specified) it would need some way to easily add additional tables for new ships and weapons. Something as simple as allowing you to turn on or turn off unofficial VP files, and automatically loading in all .tbl files in 'mod' VP files that are activated could work. Or, the mod itself could contain an initialiser file containing a list of all TBL files that need to be loaded. Of course, each modder would have to follow standard naming protocols to avoid conflicts with multiple enabled mods.